b935ed0df1
Merge pull request #665 from broadinstitute/ks_force_delete_bad_symlinks
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Executing a version of the delete_maven_links.sh
2014-06-25 00:13:05 -04:00
92028027c9
Merge pull request #666 from broadinstitute/pd_merge_selectvariants_test
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Removed redundant SelectVariantsIntegrationTest, merged its only test i...
2014-06-24 21:19:46 -04:00
06d619e9aa
Removed redundant SelectVariantsIntegrationTest, merged it's only test into protected version
2014-06-24 18:59:59 -04:00
45d819a00e
For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase.
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Better than running it during the "clean" phase, since these users may not run "mvn clean" before attempting to build.
2014-06-25 02:32:15 +08:00
42cfa3b53b
Merge pull request #664 from broadinstitute/ks_picard_maven_gatk_root
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Fixed gatk-root path in private/picard-maven/pom.xml
2014-06-24 18:48:40 +08:00
bffc9fbabd
Fixed gatk-root path in private/picard-maven/pom.xml
2014-06-24 18:45:51 +08:00
c191103326
Merge pull request #663 from broadinstitute/pd_jexl_user_exception
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Recast the "Invalid JEXL expression detected" error in SelectVariants fr...
2014-06-20 17:17:54 -04:00
65eeb4a7ab
Recast the "Invalid JEXL expression detected" error in SelectVariants from a RuntimeException to a UserException
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- PT 68931448
2014-06-20 00:05:23 -04:00
db7dc8ab5f
Merge pull request #660 from broadinstitute/pd_catvariants_list
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Added functionality to CatVariants to process .list files with -V
2014-06-19 23:54:03 -04:00
da5e567b73
Added functionality to CatVariants to process .list files with -V
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- Pivotal 70305712
2014-06-19 21:46:13 -04:00
da1dab6c32
Merge pull request #661 from broadinstitute/jw_allele_balance_gvcf
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Enable AB annotation in reference model pipeline. Incorporates patches f...
2014-06-19 13:10:41 -04:00
41d2a793f0
Merge pull request #662 from broadinstitute/eb_Carlos_Borroto_commits
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Eb carlos borroto commits
2014-06-19 12:49:14 -04:00
1092dd6e25
From Carlos Barroto: switch outputRoot in SplitSamFile to an empty string instead of null.
2014-06-19 11:06:55 -04:00
9212edba41
From Carlos Barroto: made 'level' in Picard's CalculateHsMetrics Scala Queue extension an argument.
2014-06-19 11:06:50 -04:00
8b75428a90
Enable AB annotation in reference model pipeline. Incorporates patches from John Wallace to public github account
2014-06-19 09:35:04 -04:00
2df2a153e6
Merge pull request #658 from broadinstitute/ldg_PbyTwithPriors
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Updated CalculateGenotypePosteriors to compute genotype posteriors using...
2014-06-18 15:04:39 -04:00
9640d5d745
Merge pull request #649 from broadinstitute/pd_genotypegvcf_args
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Refactored StandardCallerArgumentCollection to expose args to GenotypeGVCFs
2014-06-18 11:36:13 -04:00
2356d5d63f
Updated CalculateGenotypePosteriors to compute genotype posteriors using likelihoods from all members of the trio.
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(Right now it only works if all members of the trio are called.)
Takes posteriors as input, defaulting to PLs
Added annotations for possible de novos for us in full genotype refinement pipeline
Added family priors to CGP integration test.
Changed CGP to use PP tag instead of GP tag because posteriors are Phred-scaled. Updated CGP integration test md5s to reflect change.
2014-06-18 11:17:15 -04:00
7570666f2a
Merge pull request #655 from broadinstitute/nfd_mathutil_opts
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Optimization of function to calculate the logged sum of exponentiated values
2014-06-17 17:07:42 -04:00
5e258bfeff
Minor optimization to function to calculate the log of exponentials.
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* Avoids calling Math.Pow whenever possible (skips -Inf and 0 values),
leads to better performance.
2014-06-17 15:26:10 -04:00
0ce28b78e0
Merge pull request #657 from broadinstitute/rp_ref_model_pipeline_noMQ_indels
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Using MQRanksum for indels was a bad idea according to the knowledgebase...
2014-06-16 11:29:11 -04:00
9390c56d52
Using MQRanksum for indels was a bad idea according to the knowledgebase. Removing from the ref model pipeline. Indels create mapping quality biases that aren't indicitive of error.
2014-06-16 11:28:33 -04:00
2e78815055
Added missing arguments to GenotypeGVCFs
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- New arguments are nda, hets, indelHeterozygosity, stand_call_conf, stand_emit_conf, ploidy, and maxAltAlleles
- Addresses PT 70110918
- To do this, moved those arguments out of the StandardCallerArgumentCollection into a new GenotypeCalculationArgumentCollection, which is now included as a member of SCAC
2014-06-16 08:10:54 -04:00
838304cc89
Merge pull request #656 from broadinstitute/cww_fastSiblingIBD
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Added licenses to siblingibd classes
2014-06-13 11:37:31 -04:00
01380d20a5
Added licenses to siblingibd classes
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touch files to add licenses
2014-06-13 10:11:42 -04:00
164d270447
Merge pull request #651 from broadinstitute/cww_fastSiblingIBD
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Created a new tool, SiblingIBD, which finds Identical-By-Descent regions...
2014-06-13 09:51:33 -04:00
ba1d23e535
Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings.
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-When parental genotypes are available, implements an HMM on genotype observations in the quartet.
-Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state.
-Includes an experimental heuristic based mode for when parental genotypes are not available.
-Made a method in MendelianViolation public static to reuse code.
-Added the mockito library to private/gatk-tools-private/pom.xml
2014-06-13 09:41:37 -04:00
fbc75c8e14
Merge pull request #654 from broadinstitute/rp_gvcf_indexing_strategy
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Adding the required GVCF indexing strategy arguments.
2014-06-12 10:45:25 -04:00
b61b16ac6d
Adding the required GVCF indexing strategy arguments.
2014-06-12 10:41:36 -04:00
5493126034
Merge pull request #653 from broadinstitute/rp_updated_ref_model_qscript
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Updating the ref model pipeline qscript.
2014-06-12 09:52:17 -04:00
58e9e7df95
Updating the ref model pipeline qscript.
2014-06-12 09:51:33 -04:00
3079755b4c
Merge pull request #646 from broadinstitute/ks_disable_distribution_with_private
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Add maven -Pgsadev flag to build private jars only
2014-06-11 11:00:31 -04:00
f082572593
If passed -Pgsadev, don't build the distribution package.
2014-06-10 23:33:33 -04:00
a20da6b9aa
Merge pull request #650 from broadinstitute/xhmm_Qscript
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For XHMM and Depth-of-Coverage Qscripts, add ability for user to input s...
2014-06-10 10:20:21 -04:00
a1868e8b82
For XHMM and Depth-of-Coverage Qscripts, add ability for user to input sample renaming file at the GATK level using existing GATK flag (--sample_rename_mapping_file) and custom pre-processing code. For XHMM Qscript, add scatter-gather for Discovery and Genotype stages.
2014-06-09 23:49:54 -04:00
ea98a59c78
Stop downloading GATK reports from legacy AWS account
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Our old AWS account is due to be deactivated today. Starting tonight,
we'll no longer attempt to download GATK reports from it.
2014-06-06 15:19:28 -04:00
4ea53f7132
Merge pull request #647 from broadinstitute/pd_output_dir_check
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Ensure that output files are specified in a writeable location
2014-06-03 10:07:24 -04:00
4eb9858461
Ensure that output files are specified in a writeable location
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-PT 69579780
2014-06-02 21:13:59 -04:00
db96891d4b
Merge pull request #638 from broadinstitute/vrr_createTempFile_testfix
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Changed File.createTempFile to BaseTest.createTempFile calls Test
2014-05-29 10:15:05 -04:00
07567fdae3
Removed debug code outputing files not removed after VM exists in ReadThreadingLikelihoodCalculationEngineUnitTest.
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Notice however that this should not be the cause of resent problems as the code was desactivated.
2014-05-28 19:03:25 -04:00
938172d7f0
Removed redundant overrride createTempFileFromBase (same code as super class) and added some finals to DepthOfCoverageB36IntegrationTest
2014-05-28 19:02:04 -04:00
e0c221470c
Changed File.createTempFile to BaseTest.createTempFile
2014-05-28 18:59:48 -04:00
ef7531d4a5
Merge pull request #640 from broadinstitute/IntegerSWImplementation
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Change SmithWaterman to use integers instead of doubles.
2014-05-28 15:10:05 -04:00
cc45e62e8e
Change SmithWaterman to use integers instead of doubles.
2014-05-28 13:13:14 -04:00
ac52fa581a
Merge pull request #644 from broadinstitute/ks_queue_test_temp_fix
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Disabled ExampleUG Queue Tests, fixed internal extensions dependency.
2014-05-28 11:29:08 -04:00
ff43b1f298
Merge pull request #636 from broadinstitute/pd_log10_refactor
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Replaced the static, fixed MathUtils.log10Cache array with a dynamic Log...
2014-05-28 08:46:49 -04:00
ed66f690dd
Merge pull request #645 from broadinstitute/pd_progress_format
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Legibility improvements to ProgressMeter
2014-05-28 08:45:26 -04:00
6122b2805d
Legibility improvements to ProgressMeter
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- Fields in the header are delimited with the pipe character
- Header is now split into two lines to improve spacing
- Field width in header and progress lines auto-adjusts to length of "processing units" label (sites, active regions, etc)
- Addresses PT 69725930
2014-05-27 23:52:42 -04:00
c15e6fcc0e
Refactored the static lookup arrays in MathUtils (log10Cache, log10FactorialCache, jacobianLogTable)
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-They are now only computed when necessary
-Log10Cache is dynamically resizable, either by calling get() on an out-of-range value or by calling ensureCacheContains
-Log10FactorialCache and JacobianLogTable are initialized to a fixed size on first access and are not resizable
-Addresses PT 69124396
2014-05-27 22:27:57 -04:00
b77589696e
Merge pull request #643 from broadinstitute/rp_remove_hwp
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Removing HWP from GenotypeSummaries because of integer overflow issues w...
2014-05-27 17:21:19 -04:00
droazen
Eric Banks
Phillip Dexheimer
Khalid Shakir
kshakir
Ryan Poplin
Laura Gauthier
Nigel Delaney
Nigel Delaney
Chris Whelan
Menachem Fromer
jmthibault79
Valentin Ruano Rubio